Genetic Variant DAPL1:c.224+7_224+8insATATATATATATATATATATATATATATATAT (chr2-158826494-C-CATATATATATATATATATATATATATATATAT) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The ENST00000343761.4(DAPL1):c.224+7_224+8insATATATATATATATATATATATATATATATAT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00041 ( 0 hom., cov: 14)

Exomes 𝑓: 0.000045 ( 3 hom. )

Failed GnomAD Quality Control

Consequence

DAPL1
ENST00000343761.4 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0920

Variant links:

Genes affected

DAPL1 (HGNC:21490): (death associated protein like 1) Predicted to enable death domain binding activity. Predicted to be involved in apoptotic signaling pathway; cellular response to amino acid starvation; and negative regulation of autophagy. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

DAPL1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAPL1	ENST00000343761.4 link	c.224+7_224+8insATATATATATATATATATATATATATATATAT		splice_region_variant, intron_variant	Intron 3 of 3	3		ENSP00000385306.2		H0Y3U5
DAPL1	ENST00000409042.5 link	c.299+7_299+8insATATATATATATATATATATATATATATATAT		splice_region_variant, intron_variant	Intron 4 of 4	4		ENSP00000386422.1		B8ZZC6

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

60270

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000484

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000526

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000264

Gnomad SAS

AF:

0.000498

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000421

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000446

AC:

AN:

201834

Hom.:

Cov.:

AF XY:

0.0000454

AC XY:

AN XY:

110022

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.000348

Gnomad4 NFE exome

AF:

0.0000237

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000415

AC:

AN:

60312

Hom.:

Cov.:

AF XY:

0.000327

AC XY:

AN XY:

27504

show subpopulations

Gnomad4 AFR

AF:

0.000483

Gnomad4 AMR

AF:

0.000525

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000265

Gnomad4 SAS

AF:

0.000501

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000421

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

2-158826494-CATATATATATAT-CATATATATATATATATATATATATATATATATATATATATATAT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over